From f1782c8002dbed0781be81f244a9bf2acc637a5b Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Sun, 28 Aug 2022 15:13:03 +0100
Subject: [PATCH] preseq: init

---
 BioArchLinux/preseq/PKGBUILD   | 29 +++++++++++++++++++++++++++++
 BioArchLinux/preseq/lilac.py   | 12 ++++++++++++
 BioArchLinux/preseq/lilac.yaml | 14 ++++++++++++++
 3 files changed, 55 insertions(+)
 create mode 100644 BioArchLinux/preseq/PKGBUILD
 create mode 100644 BioArchLinux/preseq/lilac.py
 create mode 100644 BioArchLinux/preseq/lilac.yaml

diff --git a/BioArchLinux/preseq/PKGBUILD b/BioArchLinux/preseq/PKGBUILD
new file mode 100644
index 0000000000..4cea6d565d
--- /dev/null
+++ b/BioArchLinux/preseq/PKGBUILD
@@ -0,0 +1,29 @@
+# Maintainer: Grey Christoforo <first name [at] last name [dot] net>
+
+pkgname=preseq
+pkgver=3.1.2
+pkgrel=1
+pkgdesc="A tool for predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth."
+arch=('x86_64')
+url="http://smithlabresearch.org/software/preseq/"
+depends=('gsl' 'htslib')
+makedepends=('make')
+license=('GPL3')
+source=("https://github.com/smithlabcode/preseq/releases/download/v${pkgver}/preseq-${pkgver}.tar.gz")
+md5sums=('fca0d3e94ce2b557d3b2d6f374498bcc')
+
+prepare() {
+  cd "${pkgname}-${pkgver}"
+  ./configure --prefix="${pkgdir}/usr" --enable-hts
+}
+
+build() {
+  cd "${pkgname}-${pkgver}"
+  make all
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+  make install
+}
+
diff --git a/BioArchLinux/preseq/lilac.py b/BioArchLinux/preseq/lilac.py
new file mode 100644
index 0000000000..c6d1de3db7
--- /dev/null
+++ b/BioArchLinux/preseq/lilac.py
@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+  update_aur_repo()
diff --git a/BioArchLinux/preseq/lilac.yaml b/BioArchLinux/preseq/lilac.yaml
new file mode 100644
index 0000000000..67402f0cce
--- /dev/null
+++ b/BioArchLinux/preseq/lilac.yaml
@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - source: github
+    github: smithlabcode/preseq
+    use_latest_release: true
+    prefix: 'v'
+  - alias: alpm-lilac
+    alpm: htslib
+    strip_release: true
+repo_depends:
+  - htslib